Project: Hunters
by TheDusty321
Summary: After Samus destroys the BSL Station, the Federation creates clones of Samus to bring her in for her crimes against them. However, the clones escape and decide to go find Samus, not to harm her, but to help her. Will they get to her before the Federation finds them, or will they pay the price for their betrayal?
1. Prologue

**I do not own the Metroid series. Nintendo does. I only own this story. Enjoy!**

* * *

_Location: A lab at Federation HQ, Earth_

Two Federation scientists were working on a rather ambitious project for their superiors. "What is this project?" you may ask. Well, after the bounty hunter Samus Aran destroyed the BSL (Biologic Space Laboratories) Research Station, it was the final straw and thus the Galactic Federation deemed her an outlaw. When devising ways to bring her in, they came up with an idea. Create clones of Samus to match her and subdue her as a result, bringing her back to HQ to be tried for her crimes against the Federation. A few individuals within the Federation, such as Admiral Castor Dane and Anthony Higgs, spoke out against the idea. They were promptly stripped of their respective statuses and then imprisoned. With all of the opposition dealt with, they charged these two scientists with the task of creating these clones.

Which brings us back to the present scene. The two scientists were looking at their handiwork and were quite proud. By now, the clones were about finished and were soon to be awakened. The one on the scientists' right looked like Samus' doppelganger, minus her slightly pale skin and black hair. The one on the left, however, looked like a much younger version of Samus, also with slightly pale skin and with green hair. Their resemblance to Samus is easily explained, as they were both created from Samus' DNA. However, despite their appearance, they are not normal humans. Along with the human and Chozo DNA received from Samus, they also have Metroid DNA. You see, the clone on the right was created from what was left of Dark Samus, taken off of Samus' PED (Phazon Enhancement Device). While the clone on the left was created from what was left of the Super Metroid, the one that imprinted on Samus and ended up giving its life to help her defeat Mother Brain once and for all. These samples were taken off of Samus' Varia Suit, much like the ones used to create the Metroid clones on the Bottle Ship and BSL Station and the Metroid vaccine that saved Samus' life when an X Parasite infected her. The samples from both Dark Samus and the Super Metroid were then combined with Samus' DNA to create the clones. The scientists were hoping that the clones would be obedient and not turn on them like some of the other Federation creations have before them, like their clone of the Space Pirate Ridley and MB, an android version of Mother Brain created to control the Metroid clones. The scientists were sure they would follow the Federation's orders and bring Samus to them.

However, what the scientists didn't realize is that while the clones have the abilities of their counterparts, they also have their consciousness and were using telepathy to not only get to know each other, but also to plan their escape.


	2. Awakening

_Location: Federation lab, Earth_

Two days later, the clones were ready to be awakened and they were in perfect health.

"They're ready! Drain their tanks!" commanded one of the scientists, Roger Griffith.

The other scientist, Jason Smith, complied.

"Draining the tanks now!" he said pressing the buttons to drain the two tanks.

They watched the green liquid drain out of the tanks the clones were in. Soon enough, the tanks were empty and the glass tubes could now be opened. No longer floating in liquid, the clones were slumped against the glass, so the scientists were careful opening the tanks. The scientists caught the clones as they fell without the glass to support their bodies. Each scientist carried a clone to a nearby operating table. They laid the clones onto the table, with the clones lying on their backs. With that done, they checked the clones' vitals, just in case. Their vitals were A-Okay. As you might have guessed, a lot was riding on this project. Failure wasn't an option.

The scientists waited with bated breath. They didn't wait long. They heard a groan coming from the Dark Samus clone. She was waking up. Sure enough, she slowly opened her eyes, only to shut them in response to the bright light above her and raise her left arm to block it. She turned her head away from the light towards the scientists and opened her eyes again. She saw the scientists and got up into a sitting position. The scientist's were amazed at her intelligence and decided to greet her.

"Hello." They said to her.

She turned back to them and replied in kind. The scientists were really amazed now. They decided to ask her something.

"Can you stand?" They asked her.

"Of course." The clone said to them and stood up off the table. "Is there anything else you wanna ask me?" She asked them.

The scientists looked at each other. They nodded to each other and decided to ask her something that's been bothering them since the clone's response to their greeting.

"How is it that you can talk?" Jason asked the clone.

She walked up to them and answered, "Because I am Dark Samus and me and the little one will be taking our leave if you don't mind."

Before they could express their shock, Dark Samus grabbed their heads and bashed them together, knocking the scientists unconscious. With that done, she went to the other side of the table and shook her companion in order to wake her up. The clone of the last Metroid let out a little groan as she woke up. She opened her eyes and saw Dark Samus hovering over her.

"Mumu?" ("Mama?") The little one asked. Unlike Dark Samus, who was able to talk since she first encountered the Space Pirates on their way to Aether and only got better at it after encountering Samus and controlling Aurora Unit 313, the Metroid hatchling was never able to, not having a mouth or a human form at the time. However, it has listened to Samus talk long enough to know how to talk as well. Dark Samus shook her head.

"Hate to disappoint you, little one, but I'm not Samus. I'm Dark Samus. However, as I promised, we'll go find her." She said to the child.

The hatchling, a little more awake now, nodded her head in understanding. Though, there was still a problem.

"Uh cen't floot." ("I can't float.") Said the hatchling sadly.

Dark Samus, though she mostly floated, was able to walk ever since she was reborn in her humanoid form. She had learned it from watching Samus dodge her attacks as Metroid Prime, as well as from watching the Space Pirates travel to and fro on their frigate. Everything else was all from mimicking Samus. But, once again, the Metroid hatchling never had a humanoid form, so it couldn't do anything other than float.

"Don't worry," Dark Samus said to her, "I'll help you move your new body. It's easy once you get a hang of it. I'll help you form your words better while I'm at it."

With that said, Dark Samus began teaching the hatchling how to turn her head, then move her torso, and then her arms. All the while teaching her how to form words. After a while, the child was able to move her upper half on her own and was able to talk more clearly. All that was left was to teach the hatchling to walk. With that in mind, she picked up the hatchling under her arms and set her down on her feet, much like a real mother would her toddler. It took the little Metroid a while to get used to even having legs at all. However, with Dark Samus' coaching, she soon stood, albeit a little wobbly. Dark Samus told the little Metroid that she would get better as she does it, like she did. After falling a couple of times, the hatchling soon got the hang of walking on two legs.

With that done, Dark Samus looked at a piece of paper she had found while teaching the hatchling to walk. On it were the names that the scientists planned on giving them. The hatchling was curious as to what Dark Samus was looking at.

"It's the names that those two scientists were planning on giving us." Dark Samus explained. "Looks like I'm 'Sarah' and you're 'Sammy'. Huh, not a bad name. I like it. To be honest, I was getting sick of having Samus' name."

She looked to the little Metroid.

"'Sammy', do you like that name?" she asked the little one.

'Sammy' nodded her head.

"Yes, 'Sarah', I like it a lot!" the newly dubbed Sammy answered, talking a lot better than before.

"Good to hear it, little hatchling." Sarah replied. "Right. Now that we have our names and that you can walk and talk properly, there's still the matter of clothing, as we're still naked."

She proceeded to look around the room.

"I doubt the scientists' clothes would fit us, least of all you." She said.

Then she found a briefcase.

"Can't hurt to look inside." She said to herself.

She opened it up and found two sets of clothing, one for each of them.

"Sammy, we're in luck! These guys were prepared!" She called.

Sarah tossed the smaller set to Sammy, but was quickly at a loss as to how to put them on. She blushed in embarrassment. Sammy saw her confusion and decided that it was her turn to help.

"Sarah, watch what I do." She said to her friend.

She then slipped her legs through the holes in her new panties.

"Make sure the tag is inside and behind." She advised.

Sarah understood and put her panties on; making sure the tag was on the inside and in the rear.

"It's the same with pants." Sammy said to her, as she put her new denim shorts on.

Sarah did like her with her jeans.

"I assume this goes over my breasts." Sarah said holding up a bra.

Sammy nodded and Sarah put the bra on, though she didn't secure it and it fell off.

Sammy sighed. "Here, let me help you with that."

Sarah got down on her knees so Sammy could reach. Sammy put the bra back on and then secured it in the back. Now the bra wouldn't fall off so easily.

"How do you know how to do these things?" Sarah asked Sammy.

"I followed Samus everywhere before she sent me to the Ceres Space Colony, so I've watched her dress herself a few times." Sammy explained.

"Oh." Said Sarah.

Sammy put on her bra as well, though she didn't really need it. They moved on to the shirts. By now, Sarah was getting it and was happy for it. Same for socks and shoes. With that, both clones were fully clothed. Now, all that was left to do was get out of Federation HQ and find a ship to get off of Earth and start looking for Samus. That was, until Sammy made an announcement.

"I'm hungry." She groaned as her stomach growled.

Sarah facepalmed when she realized something.

"Of course. Neither one of us has eaten anything since waking up." She said.

She looked around.

"Damn, there's no food." She said.

Then she saw the scientists and had an idea. It was a tad cruel, but it would quickly solve their hunger problem, at least for a while. She smirked.

"Hey, Sammy. What say we suck these scientists dry?" She suggested to her young companion.

Sammy was shocked.

"But they're people!" She protested.

Sarah frowned at her.

"Yeah, people who would've used us to bring down your mother. That alone makes it the right thing to do. Plus, those two made us, so they might know how to bring us down. If we eliminate them, we'll have a better chance at being safe from the Federation. Besides, it alleviates our hunger. Also, I may not have been a Metroid for a long time, but if I remember correctly, it's what Metroids do. The bottom line is, it's what's best for us."

Sarah's expression softened.

"You won't regret it. You'll see."

Sammy still wasn't sure she wanted to do it, but she knew that Sarah was right. It had to be done.

"Okay." She sighed. "I'll do it."

Sarah smiled.

"Atta girl." She said. "Let the feast begin." She declared.

With that, the two of them bit into the scientists' heads and leeched away all of their life energy. When they were finally done, the scientists were nothing more than dry husks, mere shells of what they used to be. Sarah and Sammy were both satisfied and wouldn't go hungry for a while, for the scientists had a lot of energy in their bodies. Sammy still felt guilty, but knew it was the right thing to do. Sarah got down on her knees and spoke to her.

"Hey." She said. "Now that we're full, let's go find a ship and get out of here. Okay?"

Sammy looked at her and nodded. With that, the two Metroids at last vacated the laboratory in search of the ship that would take them to Samus.


	3. The Escape

_Location: Federation HQ, Earth_

Two Metroids-turned-human clones were currently sneaking around the headquarters in search of a ship to get them off of the planet, so they can start their search for Samus Aran. They decided the best place to start is Hangar Alpha, the nearest hangar. They were on their way there now, following a map they had found in a storage room. They had also armor and weapons. So far, no one had seen them. But how long will that last? Sammy would rather not think about it.

At last, they reached the doors to the hangar. Unfortunately, they needed a Level 2 Keycard just to get in.

"Damn. Now what are we going to do?" Sarah asked.

Sammy went to lean against the wall the doors were on, when her elbow hit a loose bit. Curious, she discovered a secret compartment. And what was inside, but the Level 2 Keycard they needed. Sammy jumped for joy.

"Sarah, look what I have." She said.

Sarah saw the card and was agape.

"A Level 2 Keycard. Awesome. Now we can get into the hangar." She said.

She let Sammy slip the card into the slot and the doors opened. They went through the doors to a small corridor to an elevator shaft. They got to the elevator and took it down to the hangar itself. They got out and saw a few ships docked in the bay. One in particular looked just like one of Samus' previous gunships, except it was steel gray and had a blue visor. Sammy liked this one a lot, because it reminded her of Samus. Sarah liked it too, but for a different reason. That reason being that it was reminiscent of her suit as Dark Samus. They agreed to take this one.

"You know, Sammy. This was almost too easy." Sarah said as they walked towards the gunship.

As fate would have it, as soon as she said that, the alarm went off.

"Damn. Someone found out we escaped. Tsk, took them long enough. Come on, Sammy. Let's get out of here." Sarah said.

They then ran to the gunship, making it inside before they heard someone coming down the elevator.

"No time to set coordinates. Let's just get out of this place." Sarah said as she took the controls.

Sammy nodded and took the spare seat. Sarah got the gunship off the floor and heading out of the hangar. A Federation guard came out of the elevator and saw this happening.

"Do you read me? Our new gunship's being stolen! Must be the clones that escaped!" The guard reported via comm link.

"The gunship that was made for them in Hangar Alpha, correct?" asked another guard.

"Yes, that's correct!" replied the first guard.

"Got it! We'll prepare to shoot it down! Those clones must not be allowed to escape!"

With that, the Federation guards prepared their anti-aircraft cannons to fire upon the renegade gunship.

"Sammy, they're going to try to shoot us down, so hang on! It's going to be a bumpy ride!" Sarah commanded from her chair.

Sammy nodded and held on as tight as she could. Once the gunship was out of the hangar and in range of the cannons, the guards started firing at the gunship. Sarah swerved to and fro to avoid the cannon fire. This went on until the gunship made it into the atmosphere. Fortunately, there wasn't a scratch on it. Both Sarah and Sammy let out a sigh of relief as they entered space.

"Now, Sammy, just because we're off the planet, doesn't mean we're safe. They can still follow us via starship. The only way to lose them is to make a hyperspace jump to somewhere far away. Where exactly, I haven't a clue." Sarah said.

Sammy piped up. "Look in the Federation database. There might be a planet we can go to."

"Funny. I was about to do just that. And, don't forget, I once stole an Aurora Unit, so it'll be easy to get in there." Sarah said.

"That will not be necessary. We will provide our assistance in this matter." Said a voice.

This startled both of the clones. They were soon greeted by a holographic image of an Aurora Unit.

"Wait. That voice. You're… 242, right?" Sarah asked.

"That is correct, young Sarah. And as was said before, we will provide our assistance to you."


	4. Escaping to Tallon IV

_Location: Aran Gunship, Solar System_

"So let me get this straight. You're going to help us escape?" Sarah asked in surprise.

"That is correct. We recognize that the Galactic Federation is not what it used to be. There are individuals within the Federation who think that they can control such dangerous creatures such as Metroids, X Parasites, and Space Pirates like Ridley. All attempts to do so have consistently ended in failure, as they were created to be unstoppable. Had Samus not intervened, the bioweapons could've spread to the rest of the galaxy and eventually Earth, slaughtering every last person on the planet. As such, we think it is foolhardy to create weapons that you cannot counter if need be. Because of this, we will no longer assist those who take such foolish actions. This is why we will assist you in finding Samus. According to her ship's logs, she is currently on Tallon IV, your planet of origin, Sarah. The Federation has expressed no desire in following her, as it would have assigned you that task had you not escaped. Go now, before the Federation decides to send its Marines there. We wish you the best of luck."

With that, the image of 242 faded away, leaving Sarah and Sammy very surprised.

"Who was that?" asked Sammy.

"242. The Aurora Unit that serves on the G.F.S. Olympus, I believe. Aurora Units are organic supercomputers that make up the Federation's computer network. They can be equipped with male, female, or gender-neutral personas, based on the needs of the staff they serve. AU 242, for example, has a female persona. AU 313, the Aurora Unit I had the Space Pirates steal, was gender-neutral. They have power over ships and other kinds of machinery and even planets like Phaaze. Also, all Aurora Units are connected to one another. As a result, they have access to a rather expansive database that is unparalleled. I could go on, but I think I've said enough." Sarah explained.

"How do you know all of that?" Sammy asked her.

"I learned it all from 313. Didn't think it was important at the time." Sarah answered. "Now, enough chatter. It's high time we left. To Tallon IV!"

With that, Sarah set the coordinates for the jump into hyperspace and the gunship made the jump just as a small fleet of Federation ships came into view.

"Damn it! Those wretched clones slipped through our fingers again!" yelled James Kirk, the Commander of one of the ships.

"Calm yourself, Kirk!" called Admiral Jean-Luc Picard, the man in charge of the G.F.S. Atlantis.

"We know where they are headed! Tallon IV, the planet that the bounty hunter Samus Aran is currently on! All we have to do is follow them as they lead us straight to Aran! Set coordinates for Tallon IV, but don't leave yet! I suggest that we wait a few days before making the jump into hyperspace! That way, those treasonous clones will think that they're safe from us!" finished the Admiral.

"Understood sir!" replied Captain Kirk.

"Enjoy your time with Aran, you traitors. While it lasts." Admiral Picard said to himself.


	5. Arriving on Tallon IV & Briefing

_Location: Tallon IV, FS-176 System_

Within orbit of the planet Tallon IV, the Aran Gunship at last came out of hyperspace. Then it proceeded down through the planet's atmosphere. Sarah and Sammy were not the same as when they came in.

You see, whilst they were in hyperspace, Sarah decided to check the Federation records on Samus' activity. She only expected to learn about what happened after the battle on Phaaze. She got that, plus Samus' first mission on Zebes. Both her and Sammy were shocked when they read about Samus' mission on SR388. This wasn't only because they were both Metroids. For Sammy, this was her real mother, the Queen Metroid, and all of her brethren being exterminated without hesitation or remorse. Not to mention by the same bounty hunter she called her mother. Needless to say, she was heartbroken. She broke down right there and then. Sarah did all she could to comfort and reassure her. Sammy cried until she fell asleep. She slept on Sarah's body for the rest of the way.

The gunship soon came out of the atmosphere to the planet below. Sarah was currently over the Overworld, searching for a place to land. She came upon the Impact Crater and gazed at it. She got a full view of the crater now that the Artifact Temple was gone. She wanted to wake Sammy up to look at it with her, but decided not to. She soon spotted a ship that she suspected to be Samus'. It was in the same place that Samus had made planetfall before. She decided it wasn't a good idea to land there, so she decided to look somewhere else. She eventually landed the gunship across the water from where the Frigate Orpheon had crashed.

Once that was done, Sarah hesitantly decided to wake little Sammy up.

"Sammy. C'mon. It's time to wake up. We're here." She whispered to the little one as she shook her a little.

Sammy groaned as she woke up. She sat up and rubbed the sleep out of her eyes. Sarah had to admit she looked very cute.

"Sarah? Are we really there already?" Sammy asked sleepily.

"Yes." Sarah answered.

This seemed to satisfy the little Metroid, as she stretched and proceeded to get up off of Sarah's lap. Sarah stood up and went to get the armor and weapons they had stolen. She came back with them and handed the smaller set to Sammy, who was a little more awake now.

"Feel better?" Asked Sarah.

Sammy looked up at her.

"A little." She answered.

Sarah gave a sad smile.

"You know, it's okay if you don't want to see Samus right now. I'll understand." She said to Sammy.

Sammy shook her head.

"No, I want to see her. I understand that it was the right thing to do." She said, referring to the extermination of the Metroids on SR388. "Sure, she killed my brethren in cold blood. She could have easily done the same to me, but she didn't. That's the reason why I saved her from Mother Brain back on Zebes. I love her too much to hate her for what's done to my kind. She's my mother and I'm her child and nothing is going to change that. Do you understand what I'm saying Sarah?"

Sarah was surprised, but chuckled.

"Sort of. I've never seen or experienced half of the things you have, like love, mercy, or compassion. It must be my new human brain that's given me these emotions. There's also the lack of Phazon Corruption because of Phaaze being destroyed. Then again, it could be that being with you brought these emotions about, like with that android MB. I guess I'll never know."

Her smile turned into a frown.

"That aside, let's go find Samus. I have a feeling the Federation is not too far behind us." Sarah finished.

"All right! Let's go!" shouted Sammy. "I'm coming back, Mama!"

Sarah chuckled at the little one's excitement and followed her to the hatch on top of the gunship.

* * *

_Location: G.F.S. Atlantis, Solar System_

Meanwhile, on the Atlantis, Admiral Picard was talking about the upcoming operation involving the apprehension of Samus and the clones.

"They will no doubt be together when we arrive. That will make capturing them easier." Explained the Admiral.

"But how?" asked a Fleet Trooper.

"I'm glad you asked. Let me explain. The Bottle Ship taught us something valuable. Creating unstoppable bioweapons is a recipe for disaster. As such, we saw to it that the clones retained the Metroid's vulnerability to the cold. Subduing them will be easy. As for Aran, we have numbers on our side. Does that answer your question?" he finished.

The Trooper nodded.

"That's good. Now then, do you all understand how this operation will go? We will leave for Tallon IV. Once we arrive, we'll send down 3 whole squads. That should be enough to subdue them. Once they're subdued, the squads will bring them here to the Atlantis. They will be locked up until we reach Federation HQ. Once there, they will be brought before the Council to await their sentence. But, I warn you. Make sure you have ice-based weaponry with you. This mission will not go smoothly without it. Also, expect some resistance. That is all. If you have any questions or concerns, feel free to ask." The Admiral explained.

"What if the Council lets them go? Surely, it won't listen to us." Asked another Trooper.

"Don't worry about that. Through my years of experience, I've gained some influence in the Federation, as have the ringleaders. The Council wouldn't dare disagree with us if they want to please the masses and keep their status. You can rest assured that Aran and the clones will suffer for their crimes. Just you wait and see." Admiral Picard said to the Trooper.

No one said anything else and went back to work. Admiral Picard looked out to the stars and smirked.

"Oh yes. They will." He murmured to himself.


End file.
